Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012716.1 Kokia drynarioides strain JFW-HI SEQ_127727, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 198044
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 110 characters in sequence are not A, C, G, or T
Found at i:3951 original size:16 final size:19
Alignment explanation
Indices: 3903--3952 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 19
3893 TTTAGTCATA
3903 TAATAAATTATTAATATAAT
1 TAATAAATTATTAATAT-AT
3923 TAATATAATTTATT-AT-T-T
1 TAATA-AA-TTATTAATATAT
3941 TAATAAATTATT
1 TAATAAATTATT
3953 TAATGTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 5 0.18
17 2 0.07
18 6 0.21
20 6 0.21
21 4 0.14
22 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATAAATTATTAATATAT
Found at i:3993 original size:15 final size:14
Alignment explanation
Indices: 3968--4007 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
3958 TTTCAATTTT
3968 ATTTT-AATAATAA
1 ATTTTAAATAATAA
3981 ATTTTAAAATAAT-A
1 ATTTT-AAATAATAA
3995 ATTTTAAATAATA
1 ATTTTAAATAATA
4008 TTCTTCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 12 0.50
14 6 0.25
15 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAAATAATAA
Found at i:4050 original size:14 final size:15
Alignment explanation
Indices: 4026--4062 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
4016 ATATTATTAA
4026 AAATA-TTTAAT-AT
1 AAATATTTTAATAAT
*
4039 TAATATTTTAATAAT
1 AAATATTTTAATAAT
4054 AAATATTTT
1 AAATATTTT
4063 GTAGTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 4 0.20
14 6 0.30
15 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:5046 original size:6 final size:6
Alignment explanation
Indices: 5037--5064 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5027 AATAATAAAT
5037 TTAATA TTAATA TTAATA TTAATA TTAA
1 TTAATA TTAATA TTAATA TTAATA TTAA
5065 ATAAATACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:5047 original size:18 final size:18
Alignment explanation
Indices: 5022--5071 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
5012 ATTTTTAAAA
5022 AATA-TAATAATAAAT-TT
1 AATATTAAT-ATAAATATT
*
5039 AATATTAATATTAATATT
1 AATATTAATATAAATATT
5057 AATATTAA-ATAAATA
1 AATATTAATATAAATA
5072 CAATTTTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATATTAATATAAATATT
Found at i:5358 original size:24 final size:24
Alignment explanation
Indices: 5326--5371 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5316 TCATTTAACT
*
5326 TAATCGAACATGTTCACGAACATA
1 TAATCGAACACGTTCACGAACATA
*
5350 TAATTGAACACGTTCACGAACA
1 TAATCGAACACGTTCACGAACA
5372 ATGTTAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (24 bp):
TAATCGAACACGTTCACGAACATA
Found at i:6131 original size:25 final size:26
Alignment explanation
Indices: 6103--6155 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
6093 GATTTTTATT
6103 TTATTGAATAATAATAT-AATTATAA
1 TTATTGAATAATAATATAAATTATAA
* ** *
6128 TTATTTAATTTTAATATAAATTTTAA
1 TTATTGAATAATAATATAAATTATAA
6154 TT
1 TT
6156 TTTATTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
TTATTGAATAATAATATAAATTATAA
Found at i:6191 original size:10 final size:10
Alignment explanation
Indices: 6153--6196 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
6143 ATAAATTTTA
6153 ATTTTTATTAT
1 ATTTTTA-TAT
*
6164 ATTTTTA-AC
1 ATTTTTATAT
*
6173 ATATTTATAT
1 ATTTTTATAT
6183 ATTTTTATAT
1 ATTTTTATAT
6193 ATTT
1 ATTT
6197 CTTTGAACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 7 0.25
10 14 0.50
11 7 0.25
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:7532 original size:19 final size:17
Alignment explanation
Indices: 7508--7586 Score: 62
Period size: 17 Copynumber: 4.9 Consensus size: 17
7498 AATTTATTGT
7508 TGTTTTGATGCTTTTTTAC
1 TGTTTTGATG--TTTTTAC
*
7527 TGTTTTGATGTTTTTAT
1 TGTTTTGATGTTTTTAC
7544 TGTTTTG--G---TTAC
1 TGTTTTGATGTTTTTAC
* *
7556 TATTTTGAT-TTCTTAC
1 TGTTTTGATGTTTTTAC
*
7572 TGTTTTGGTGTTTTT
1 TGTTTTGATGTTTTT
7587 TTTGTTGTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
12 9 0.19
15 1 0.02
16 11 0.23
17 17 0.35
19 10 0.21
ACGTcount: A:0.10, C:0.06, G:0.18, T:0.66
Consensus pattern (17 bp):
TGTTTTGATGTTTTTAC
Found at i:7562 original size:29 final size:28
Alignment explanation
Indices: 7523--7580 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
7513 TGATGCTTTT
* * *
7523 TTACTGTTTTGATGTTTTTATTGTTTTGG
1 TTACTATTTTGAT-TTCTTACTGTTTTGG
7552 TTACTATTTTGATTTCTTACTGTTTTGG
1 TTACTATTTTGATTTCTTACTGTTTTGG
7580 T
1 T
7581 GTTTTTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.12, C:0.07, G:0.17, T:0.64
Consensus pattern (28 bp):
TTACTATTTTGATTTCTTACTGTTTTGG
Found at i:7610 original size:15 final size:15
Alignment explanation
Indices: 7582--7620 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
7572 TGTTTTGGTG
* *
7582 TTTTTTTTGTTGTTA
1 TTTTTGTTGATGTTA
7597 TTTTTGTTGATGTTA
1 TTTTTGTTGATGTTA
*
7612 TTGTTGTTG
1 TTTTTGTTG
7621 TTTTGATTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.00, G:0.21, T:0.72
Consensus pattern (15 bp):
TTTTTGTTGATGTTA
Found at i:7820 original size:24 final size:25
Alignment explanation
Indices: 7774--7820 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
7764 TATAAAGAAT
*
7774 TTTTAACGTATTTTAAATTTATTAG
1 TTTTAACGTATTTTAAATGTATTAG
* *
7799 TTTTAATGT-TTTTAAGTGTATT
1 TTTTAACGTATTTTAAATGTATT
7821 TGATATATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.60
Consensus pattern (25 bp):
TTTTAACGTATTTTAAATGTATTAG
Found at i:11134 original size:22 final size:21
Alignment explanation
Indices: 11081--11135 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
11071 CTTTCGTTTG
*
11081 AATTTTTATATATTATTTTAA
1 AATTTTTATTTATTATTTTAA
**
11102 AATTTACATTTATATATTTTAA
1 AATTTTTATTTAT-TATTTTAA
11124 AATTTTTATTTA
1 AATTTTTATTTA
11136 GAAAATGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTTTTATTTATTATTTTAA
Found at i:12293 original size:7 final size:7
Alignment explanation
Indices: 12281--12311 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
12271 AAGGTGTTAG
12281 ATTGAAA
1 ATTGAAA
12288 ATTGAAA
1 ATTGAAA
12295 ATTGAAA
1 ATTGAAA
12302 ATTGAAA
1 ATTGAAA
12309 ATT
1 ATT
12312 CAGTGAGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (7 bp):
ATTGAAA
Found at i:31212 original size:26 final size:27
Alignment explanation
Indices: 31183--31240 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
31173 ATTTTTTAAA
31183 AATTTTAAAATTTT-AAATTAAAATTT
1 AATTTTAAAATTTTAAAATTAAAATTT
** *
31209 AA-TTTAATTTTTTAAAATTATAATTT
1 AATTTTAAAATTTTAAAATTAAAATTT
31235 AATTTT
1 AATTTT
31241 GACCCCCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 9 0.33
26 15 0.56
27 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
AATTTTAAAATTTTAAAATTAAAATTT
Found at i:31223 original size:20 final size:21
Alignment explanation
Indices: 31200--31240 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
31190 AAATTTTAAA
31200 TTAAAATT-TAATTTAATTTT
1 TTAAAATTATAATTTAATTTT
31220 TTAAAATTATAATTTAATTTT
1 TTAAAATTATAATTTAATTTT
31241 GACCCCCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTAAAATTATAATTTAATTTT
Found at i:34109 original size:14 final size:12
Alignment explanation
Indices: 34078--34139 Score: 70
Period size: 14 Copynumber: 4.8 Consensus size: 12
34068 TAAATCAATC
34078 TTTTCAAAAATAT
1 TTTTC-AAAATAT
34091 TTTTCAAAATCACT
1 TTTTCAAAAT-A-T
34105 TTTTCAAAATAT
1 TTTTCAAAATAT
*
34117 TTTTTAAAAGTATT
1 TTTTCAAAA-TA-T
34131 TTTTCAAAA
1 TTTTCAAAA
34140 CAATGCTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
12 14 0.33
13 9 0.21
14 20 0.47
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (12 bp):
TTTTCAAAATAT
Found at i:34113 original size:26 final size:26
Alignment explanation
Indices: 34069--34139 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
34059 TTCAAATATT
34069 AAATCAATCTTTTCAAAAATATTTTTCA
1 AAATCAAT-TTTTC-AAAATATTTTTCA
* *
34097 AAATCACTTTTTCAAAATATTTTTTA
1 AAATCAATTTTTCAAAATATTTTTCA
*
34123 AAAGT-ATTTTTTCAAAA
1 AAA-TCAATTTTTCAAAA
34140 CAATGCTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 26 0.67
27 6 0.15
28 7 0.18
ACGTcount: A:0.42, C:0.11, G:0.01, T:0.45
Consensus pattern (26 bp):
AAATCAATTTTTCAAAATATTTTTCA
Found at i:42570 original size:24 final size:26
Alignment explanation
Indices: 42543--42598 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
42533 GTATTTTTGA
*
42543 TTTTATTTT-TT-TGAA-TTTTATAGT
1 TTTTATTTTGTTATAAATTTTTAT-GT
42567 TTTT-TTTTGTTATAAATTTTTATGT
1 TTTTATTTTGTTATAAATTTTTATGT
42592 TTTTATT
1 TTTTATT
42599 AAAAATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 4 0.15
24 6 0.22
25 9 0.33
26 8 0.30
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (26 bp):
TTTTATTTTGTTATAAATTTTTATGT
Found at i:42960 original size:15 final size:15
Alignment explanation
Indices: 42940--42998 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
42930 TGATAAATTG
*
42940 AAAAATTAAGTCTTA
1 AAAAATTAAGTATTA
*
42955 AAAAA-TAAGTGTTGAAA
1 AAAAATTAAGTATT---A
42972 AAAAATTAAGTATTA
1 AAAAATTAAGTATTA
*
42987 AAAAGTTAAGTA
1 AAAAATTAAGTA
42999 CGTTTAAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 7 0.19
15 17 0.46
17 6 0.16
18 7 0.19
ACGTcount: A:0.58, C:0.02, G:0.12, T:0.29
Consensus pattern (15 bp):
AAAAATTAAGTATTA
Found at i:42963 original size:14 final size:15
Alignment explanation
Indices: 42937--42974 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
42927 GTTTGATAAA
*
42937 TTGAAAAATTAAGTC
1 TTGAAAAAATAAGTC
*
42952 TT-AAAAAATAAGTG
1 TTGAAAAAATAAGTC
42966 TTGAAAAAA
1 TTGAAAAAA
42975 AATTAAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (15 bp):
TTGAAAAAATAAGTC
Found at i:44133 original size:21 final size:22
Alignment explanation
Indices: 44095--44152 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
44085 AAACGATAAA
*
44095 TTTAATTTTTAATATTTATGT-TT
1 TTTAA-TTTAAAT-TTTATGTATT
*
44118 TTTAATTTAAATTTTATTTATT
1 TTTAATTTAAATTTTATGTATT
44140 TTTAA-TTAAATTT
1 TTTAATTTAAATTT
44153 AACTTTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 14 0.44
22 13 0.41
23 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTAATTTAAATTTTATGTATT
Found at i:47974 original size:5 final size:5
Alignment explanation
Indices: 47964--47988 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
47954 CTTAAATTGT
47964 ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA
47989 TATGATCAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTTA
Found at i:49502 original size:27 final size:28
Alignment explanation
Indices: 49465--49530 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
49455 ATATATATGT
* * *
49465 AATTATT--TATATTTAATAATATAA-G
1 AATTATTAATATAATTAATAAAATAATA
49490 AATTATTAATATAATTAATAAAATAATA
1 AATTATTAATATAATTAATAAAATAATA
49518 AATTATTTAATAT
1 AATTA-TTAATAT
49531 TATATTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.21
27 15 0.44
28 5 0.15
29 7 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
AATTATTAATATAATTAATAAAATAATA
Found at i:49572 original size:15 final size:16
Alignment explanation
Indices: 49545--49574 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
49535 TTTTTATTTA
49545 AATAATAAGTTTTAAC
1 AATAATAAGTTTTAAC
49561 AATAAT-AGTTTTAA
1 AATAATAAGTTTTAA
49575 ATTTTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (16 bp):
AATAATAAGTTTTAAC
Found at i:49689 original size:24 final size:24
Alignment explanation
Indices: 49620--49700 Score: 62
Period size: 23 Copynumber: 3.4 Consensus size: 24
49610 TAATTATATT
*
49620 AATATTTTATTA-ATAAATATATATTA
1 AATATTTTATAACATAAA-ATA-A-TA
**
49646 AA-A-TTTATAGACATTTAATAATA
1 AATATTTTATA-ACATAAAATAATA
*
49669 AATATTTTATAACATAAAAT-ATG
1 AATATTTTATAACATAAAATAATA
49692 AATATTTTA
1 AATATTTTA
49701 ACGATATAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
23 15 0.33
24 14 0.31
25 11 0.24
26 5 0.11
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
AATATTTTATAACATAAAATAATA
Found at i:49699 original size:23 final size:24
Alignment explanation
Indices: 49669--49721 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
49659 TTTAATAATA
49669 AATATTTTATAAC-ATA-AAATATG
1 AATATTTT-TAACGATATAAATATG
49692 AATA-TTTTAACGATATAAATATG
1 AATATTTTTAACGATATAAATATG
*
49715 AACATTT
1 AATATTT
49722 GTTTAAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.15
22 6 0.23
23 14 0.54
24 2 0.08
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (24 bp):
AATATTTTTAACGATATAAATATG
Found at i:51107 original size:19 final size:19
Alignment explanation
Indices: 51083--51120 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
51073 CATAAAAAAA
51083 TTTCATAATTGA-TACATAT
1 TTTCATAATT-ATTACATAT
*
51102 TTTCATTATTATTACATAT
1 TTTCATAATTATTACATAT
51121 AACTACACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.34, C:0.11, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTCATAATTATTACATAT
Found at i:54167 original size:25 final size:28
Alignment explanation
Indices: 54137--54196 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 28
54127 CATGAATTTT
54137 TAAATTC-GAAAAATAAAAA-A-GA-GAC
1 TAAATTCTG-AAAATAAAAAGATGATGAC
54162 TAAATTCTTGAAAATAAAAAGATGATGAC
1 TAAATTC-TGAAAATAAAAAGATGATGAC
54191 TAAATT
1 TAAATT
54197 TCAAATGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
25 7 0.23
26 10 0.33
27 2 0.07
28 2 0.07
29 9 0.30
ACGTcount: A:0.57, C:0.07, G:0.12, T:0.25
Consensus pattern (28 bp):
TAAATTCTGAAAATAAAAAGATGATGAC
Found at i:63694 original size:19 final size:21
Alignment explanation
Indices: 63652--63694 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
63642 TCTTTTATGT
**
63652 AAAAAATATATAATTTTAGTA
1 AAAAAATATATAATTTTAAAA
63673 AAAAAAT-TA-AATTTTAAAA
1 AAAAAATATATAATTTTAAAA
63692 AAA
1 AAA
63695 TGGGATTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 2 0.10
21 7 0.35
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAAAATATATAATTTTAAAA
Found at i:80065 original size:18 final size:18
Alignment explanation
Indices: 80039--80085 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
80029 GGAGAGATTA
* *
80039 TGATGGTGACCGTAGCCG
1 TGATCGTGACCGTAGACG
* *
80057 TGATCGTGATCGTGGACG
1 TGATCGTGACCGTAGACG
80075 TGATCGTGACC
1 TGATCGTGACC
80086 ACGATCGTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.17, C:0.21, G:0.36, T:0.26
Consensus pattern (18 bp):
TGATCGTGACCGTAGACG
Found at i:83665 original size:23 final size:23
Alignment explanation
Indices: 83633--83692 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
83623 CATGAACATT
* *
83633 ATGAACATGTTCGTTTAATGTT-C
1 ATGAATATGTTCGTTTAA-GTTAA
* *
83656 GTGAATATGTTCGATTAAGTTAA
1 ATGAATATGTTCGTTTAAGTTAA
83679 ATGAATATGTTCGT
1 ATGAATATGTTCGT
83693 GAATATTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 3 0.10
23 27 0.90
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (23 bp):
ATGAATATGTTCGTTTAAGTTAA
Found at i:83701 original size:23 final size:23
Alignment explanation
Indices: 83657--83702 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
83647 TTAATGTTCG
* *
83657 TGAATATGTTCGATTAAGTTAAA
1 TGAATATGTTCGATGAAATTAAA
83680 TGAATATGTTCG-TGAATATTAAA
1 TGAATATGTTCGATGAA-ATTAAA
83703 CAAACGAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.39
Consensus pattern (23 bp):
TGAATATGTTCGATGAAATTAAA
Found at i:92376 original size:36 final size:36
Alignment explanation
Indices: 92329--92420 Score: 175
Period size: 36 Copynumber: 2.6 Consensus size: 36
92319 ACAAAAAAGT
92329 TAGTTGAAATTCAGTCTTATTGAGCTCAGCCATAAC
1 TAGTTGAAATTCAGTCTTATTGAGCTCAGCCATAAC
92365 TAGTTGAAATTCAGTCTTATTGAGCTCAGCCATAAC
1 TAGTTGAAATTCAGTCTTATTGAGCTCAGCCATAAC
*
92401 TAGTTGAAATTCACTCTTAT
1 TAGTTGAAATTCAGTCTTAT
92421 CTCAGACATA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (36 bp):
TAGTTGAAATTCAGTCTTATTGAGCTCAGCCATAAC
Found at i:92378 original size:21 final size:21
Alignment explanation
Indices: 92354--92413 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
92344 CTTATTGAGC
92354 TCAGCCATAACTAGTTGAAAT
1 TCAGCCATAACTAGTTGAAAT
* **
92375 TCAGTC-T---TA-TTG-AGC
1 TCAGCCATAACTAGTTGAAAT
92390 TCAGCCATAACTAGTTGAAAT
1 TCAGCCATAACTAGTTGAAAT
92411 TCA
1 TCA
92414 CTCTTATCTC
Statistics
Matches: 27, Mismatches: 6, Indels: 12
0.60 0.13 0.27
Matches are distributed among these distances:
15 6 0.22
16 4 0.15
17 2 0.07
19 2 0.07
20 4 0.15
21 9 0.33
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (21 bp):
TCAGCCATAACTAGTTGAAAT
Found at i:92431 original size:32 final size:34
Alignment explanation
Indices: 92329--92437 Score: 150
Period size: 36 Copynumber: 3.1 Consensus size: 34
92319 ACAAAAAAGT
92329 TAGTTGAAATTCAGTCTTATTGAGCTCAGCCATAAC
1 TAGTTGAAATTCAGTCTTATT--GCTCAGCCATAAC
92365 TAGTTGAAATTCAGTCTTATTGAGCTCAGCCATAAC
1 TAGTTGAAATTCAGTCTTATT--GCTCAGCCATAAC
* *
92401 TAGTTGAAATTCACTCTTA-T-CTCAGACATAAC
1 TAGTTGAAATTCAGTCTTATTGCTCAGCCATAAC
92433 TAGTT
1 TAGTT
92438 AATTATTTGT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
32 16 0.23
35 1 0.01
36 54 0.76
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (34 bp):
TAGTTGAAATTCAGTCTTATTGCTCAGCCATAAC
Found at i:94423 original size:24 final size:25
Alignment explanation
Indices: 94385--94433 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
94375 CCGACTTCAT
94385 AAGAAATAAAAGGGAAA-AAATATAA
1 AAGAAATAAAAGGGAAATAAA-ATAA
94410 AAGAAA-AAAAGGGAAATAAAATAA
1 AAGAAATAAAAGGGAAATAAAATAA
94434 TTAAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.10
Consensus pattern (25 bp):
AAGAAATAAAAGGGAAATAAAATAA
Found at i:101091 original size:23 final size:22
Alignment explanation
Indices: 101072--101181 Score: 105
Period size: 23 Copynumber: 4.9 Consensus size: 22
101062 TTGCTGTTCA
*
101072 GCACTGTGTGTGCTTACTGTTT
1 GCACTGTGTGTGCTTACTGATT
*
101094 CGCACT-TCGTGTGCCTACTGATTT
1 -GCACTGT-GTGTGCTTACTGA-TT
* * ** *
101118 GCGCTATGTGCACCTACTGATT
1 GCACTGTGTGTGCTTACTGATT
*
101140 GCACTGTGTGTGCCTACTGGATT
1 GCACTGTGTGTGCTTACT-GATT
101163 GCACTGTGTGTGCTTACTG
1 GCACTGTGTGTGCTTACTG
101182 TTTCCCATCA
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
22 18 0.25
23 52 0.71
24 3 0.04
ACGTcount: A:0.13, C:0.24, G:0.26, T:0.37
Consensus pattern (22 bp):
GCACTGTGTGTGCTTACTGATT
Found at i:101181 original size:45 final size:46
Alignment explanation
Indices: 101072--101181 Score: 127
Period size: 45 Copynumber: 2.4 Consensus size: 46
101062 TTGCTGTTCA
*
101072 GCACTGTGTGTGCTTACTGTTTCGCACTTCGTGTGCCTACTGATTT
1 GCACTGTGTGTGCTTACTGATTCGCACTTCGTGTGCCTACTGATTT
* * ** *
101118 GCGCTATGTGCACCTACTGATT-GCACTGT-GTGTGCCTACTGGA-TT
1 GCACTGTGTGTGCTTACTGATTCGCACT-TCGTGTGCCTACT-GATTT
101163 GCACTGTGTGTGCTTACTG
1 GCACTGTGTGTGCTTACTG
101182 TTTCCCATCA
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
45 32 0.63
46 19 0.37
ACGTcount: A:0.13, C:0.24, G:0.26, T:0.37
Consensus pattern (46 bp):
GCACTGTGTGTGCTTACTGATTCGCACTTCGTGTGCCTACTGATTT
Found at i:103512 original size:33 final size:33
Alignment explanation
Indices: 103475--103549 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 33
103465 CTCGGCCATA
* * *
103475 GTCTTACATTCATAATGCCATAACCCAGTTATG
1 GTCTTACATTCAGAATGCCATAACCAAGCTATG
* *
103508 GTCTTA-ACGTCAGAATGCCATAGCCAAGCTATG
1 GTCTTACA-TTCAGAATGCCATAACCAAGCTATG
*
103541 GTCATACAT
1 GTCTTACAT
103550 CTATATACAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
32 1 0.03
33 31 0.94
34 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (33 bp):
GTCTTACATTCAGAATGCCATAACCAAGCTATG
Found at i:103617 original size:102 final size:102
Alignment explanation
Indices: 103470--103697 Score: 325
Period size: 102 Copynumber: 2.2 Consensus size: 102
103460 CATGGCTCGG
* * * * *
103470 CCATAGTCTTACATTCATAATGCCATAACCCAGTTATGGTCTTAACGTCAGAATGCCATAG-CCA
1 CCATAGTCTTAC-GTCAGAATGTCATAACCCAGCTATGGTCTTAACATCAGAATGCCATAGCCCA
103534 AGCTATGGTCATACATCTATATACACT-CTCATGGTCCAA
65 A-CTATGGTCATACATCTATATACACTGC-CATGGTCCAA
* * *
103573 CCATAGTCTTACGTCAGAATGTCATAACCCAGCTATGGTTTTAACATTAGAATGTCATAGCCCAA
1 CCATAGTCTTACGTCAGAATGTCATAACCCAGCTATGGTCTTAACATCAGAATGCCATAGCCCAA
*
103638 CTATGGTCTTACATCTATATACACTGCCATGGTCCAA
66 CTATGGTCATACATCTATATACACTGCCATGGTCCAA
*
103675 CCATGGTCTTACGTCAGAATGTC
1 CCATAGTCTTACGTCAGAATGTC
103698 GCTTGTCTCC
Statistics
Matches: 113, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
102 96 0.85
103 17 0.15
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (102 bp):
CCATAGTCTTACGTCAGAATGTCATAACCCAGCTATGGTCTTAACATCAGAATGCCATAGCCCAA
CTATGGTCATACATCTATATACACTGCCATGGTCCAA
Found at i:114648 original size:2 final size:2
Alignment explanation
Indices: 114643--114669 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
114633 AAAAAAAAAA
114643 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
114670 ATTCAGACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:115652 original size:73 final size:71
Alignment explanation
Indices: 115564--115749 Score: 214
Period size: 73 Copynumber: 2.6 Consensus size: 71
115554 TCTCTCATTC
* *
115564 CTAACTCATGTACTTCACAAGGTTTGAACCTAAGATCTC-AATTCTGGAAATCAATTTAACTCTC
1 CTAACTCATGTACTTCACAGGGTTTGAACCTAAGATCTCTAAAT-TGGAAATCAATTTAA--CTC
115628 TGTCATCCT
63 TGTCATCCT
* * * * * * *
115637 CTAACCCATGAACTTCCCAGGGTCTAAACCTAATATCTCTAAATTGGAAATCGATTTAACTCTGT
1 CTAACTCATGTACTTCACAGGGTTTGAACCTAAGATCTCTAAATTGGAAATCAATTTAACTCTGT
115702 CATCCT
66 CATCCT
* * * *
115708 CTAAATTATGTACTTGA-AGGGTTTGAACCTAAGATTTCTAAA
1 CTAACTCATGTACTTCACAGGGTTTGAACCTAAGATCTCTAAA
115750 AGTCATAACA
Statistics
Matches: 93, Mismatches: 19, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
70 21 0.23
71 23 0.25
73 46 0.49
74 3 0.03
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (71 bp):
CTAACTCATGTACTTCACAGGGTTTGAACCTAAGATCTCTAAATTGGAAATCAATTTAACTCTGT
CATCCT
Found at i:124145 original size:25 final size:26
Alignment explanation
Indices: 124092--124143 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
124082 ATTCACAGTC
* *
124092 TATTTGTTTTTTCTTTTTAATTTCTT
1 TATTTCTTTTTGCTTTTTAATTTCTT
*
124118 TATTTCTTTTTGCTTTTTATTTTCTT
1 TATTTCTTTTTGCTTTTTAATTTCTT
124144 ATGTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.10, C:0.10, G:0.04, T:0.77
Consensus pattern (26 bp):
TATTTCTTTTTGCTTTTTAATTTCTT
Found at i:124153 original size:26 final size:25
Alignment explanation
Indices: 124092--124155 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 25
124082 ATTCACAGTC
124092 TATTTGTTTTTTCTTTTTAATTTCTT
1 TATTT-TTTTTTCTTTTTAATTTCTT
* *
124118 TATTTCTTTTTGCTTTTTATTTTCTT
1 TATTT-TTTTTTCTTTTTAATTTCTT
*
124144 ATGTTTTTTTTT
1 -TATTTTTTTTT
124156 GGTGTTAAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 28 0.88
27 4 0.12
ACGTcount: A:0.09, C:0.08, G:0.05, T:0.78
Consensus pattern (25 bp):
TATTTTTTTTTCTTTTTAATTTCTT
Found at i:131721 original size:30 final size:29
Alignment explanation
Indices: 131678--131735 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
131668 TTTATATAAT
*
131678 TTTTTAAAAATT-AAATTAAATTATTATTA
1 TTTTTAAAAATTAAAATAAAATT-TTATTA
*
131707 TTTTTAAGAGATTAAAATAAAATTTTATT
1 TTTTTAA-AAATTAAAATAAAATTTTATT
131736 TTGTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 9 0.36
31 9 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (29 bp):
TTTTTAAAAATTAAAATAAAATTTTATTA
Found at i:132512 original size:32 final size:32
Alignment explanation
Indices: 132449--132512 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
132439 TAATTCTAAC
*
132449 AAATTCAATTAATTAATATGAGTTATCAAATT
1 AAATTCAATTAATTAATATGAATTATCAAATT
*
132481 AAATT-AATTAACTT-ATCATGAATTATTAAATT
1 AAATTCAATTAA-TTAAT-ATGAATTATCAAATT
132513 TAAGTAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 8 0.29
32 20 0.71
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (32 bp):
AAATTCAATTAATTAATATGAATTATCAAATT
Found at i:133982 original size:3 final size:3
Alignment explanation
Indices: 133961--133994 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
133951 TTTTGAAATA
* *
133961 TAT TAT CAT TAT CAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
133995 GTGATTGGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:139691 original size:25 final size:25
Alignment explanation
Indices: 139660--139710 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
139650 CTATTTTAGA
139660 AGCATTTGCTTATTAAGTTTCATTT
1 AGCATTTGCTTATTAAGTTTCATTT
139685 AGCATTTGCTTATTAAGTTTCATTT
1 AGCATTTGCTTATTAAGTTTCATTT
139710 A
1 A
139711 TCTAAGTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (25 bp):
AGCATTTGCTTATTAAGTTTCATTT
Found at i:143552 original size:47 final size:47
Alignment explanation
Indices: 143499--143592 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
143489 GACGGTGTTA
143499 AAATATACTCTGAGAGATGGATTTTCTCTTTGAAATAAATCAAATCT
1 AAATATACTCTGAGAGATGGATTTTCTCTTTGAAATAAATCAAATCT
143546 AAATATACTCTGAGAGATGGATTTTCTCTTTGAAATAAATCAAATCT
1 AAATATACTCTGAGAGATGGATTTTCTCTTTGAAATAAATCAAATCT
143593 GAGGCAAAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (47 bp):
AAATATACTCTGAGAGATGGATTTTCTCTTTGAAATAAATCAAATCT
Found at i:146594 original size:37 final size:39
Alignment explanation
Indices: 146552--146654 Score: 117
Period size: 37 Copynumber: 2.7 Consensus size: 39
146542 ACTTGAATAT
* * *
146552 GAGATTTTGTAGGGGTTATTTGGAAAGAGATCTTG-ATC
1 GAGATTATGTAGGGATTATTTGGAAAGAGATATTGAATC
*
146590 -AGATTATGGA-GGATTATTTGG-AA-AGATATTGAATC
1 GAGATTATGTAGGGATTATTTGGAAAGAGATATTGAATC
146625 TGAGATTATGTAGGAGATTATTTGGAAAGA
1 -GAGATTATGTAGG-GATTATTTGGAAAGA
146655 AGTTTGTTCC
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
34 7 0.13
35 5 0.09
36 10 0.19
37 17 0.32
38 1 0.02
39 10 0.19
40 2 0.04
41 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (39 bp):
GAGATTATGTAGGGATTATTTGGAAAGAGATATTGAATC
Found at i:148992 original size:24 final size:22
Alignment explanation
Indices: 148949--148993 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
148939 AAGGTCGTTT
* *
148949 AATTTTCACAAATCATTTTTAA
1 AATTTTCACAAATAAATTTTAA
148971 AATTTTCAACCAAATAAATTTTA
1 AATTTTC-A-CAAATAAATTTTA
148994 TTGAATGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 1 0.05
24 11 0.58
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTTTCACAAATAAATTTTAA
Found at i:152724 original size:80 final size:80
Alignment explanation
Indices: 152571--152727 Score: 190
Period size: 80 Copynumber: 2.0 Consensus size: 80
152561 CTTAATCTCA
* * **
152571 CAAATTAGTATCTAAACAATGCAATTTTCTTATTTTGATACCTAATCTTTTTATTCAAATGTATT
1 CAAATTAGTATCTAAACAATGCAATTTTCCTATTTTGATACCTAATCTTTTTATTCAAATATACC
*
152636 TAAGTTATTTTTATT
66 TAAATTATTTTTATT
** * * * * *
152651 CAAATTAGTATCTAAACTGTGCATTTTTCGCT-TTTTGGTACGTAATTTTTTTATTGAAATATAC
1 CAAATTAGTATCTAAACAATGCAATTTTC-CTATTTTGATACCTAATCTTTTTATTCAAATATAC
152715 CTAAATTATTTTT
65 CTAAATTATTTTT
152728 TCCCCAAATT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
80 63 0.98
81 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (80 bp):
CAAATTAGTATCTAAACAATGCAATTTTCCTATTTTGATACCTAATCTTTTTATTCAAATATACC
TAAATTATTTTTATT
Found at i:164280 original size:5 final size:6
Alignment explanation
Indices: 164263--164288 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
164253 GTGTGATGAT
164263 ATAAAA ATAAAA ATAAAA ATAAAA AT
1 ATAAAA ATAAAA ATAAAA ATAAAA AT
164289 GAAATCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:168633 original size:22 final size:22
Alignment explanation
Indices: 168590--168634 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
168580 TTTTTTTTAT
* *
168590 AAAAATACATAAGATTTCATAA
1 AAAAATACATAAAAATTCATAA
168612 AAAAATACATATAAAATT-ATAA
1 AAAAATACATA-AAAATTCATAA
168634 A
1 A
168635 TTTTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAATACATAAAAATTCATAA
Found at i:173123 original size:24 final size:24
Alignment explanation
Indices: 173095--173145 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
173085 AGAAATAATC
* * *
173095 TTTCAGTTAAATTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
173119 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
173143 TTT
1 TTT
173146 AAGTCAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:173154 original size:24 final size:24
Alignment explanation
Indices: 173107--173155 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
173097 TCAGTTAAAT
* *
173107 TCTGTTTATTTGTTTCAATTAAAC
1 TCTGTTTAGTTGTTTCAATCAAAC
173131 TCTGTTTAGTTGTTT-AAGTCAAAC
1 TCTGTTTAGTTGTTTCAA-TCAAAC
173155 T
1 T
173156 TTTATTAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.51
Consensus pattern (24 bp):
TCTGTTTAGTTGTTTCAATCAAAC
Found at i:174572 original size:77 final size:77
Alignment explanation
Indices: 174446--174613 Score: 284
Period size: 77 Copynumber: 2.2 Consensus size: 77
174436 ATAAAGTGAA
* * *
174446 TAAGGATGAAAAAG-AAAAAAGAAAGGTTAGTTAGAGGGAAGAAAAAATAAGCAGTAACTAACCT
1 TAAGGATGAAAAAGAAAAAAAAAAAGATTAGTGAGAGGGAAGAAAAAATAAGCAGTAACTAACCT
174510 AGTAATTGTCTT
66 AGTAATTGTCTT
*
174522 TAAGGATGAAAAAGAAAAAAAAAAAGATTAGTGAGAGGGAAGAAAAAATAAGCGGTAACTAACCT
1 TAAGGATGAAAAAGAAAAAAAAAAAGATTAGTGAGAGGGAAGAAAAAATAAGCAGTAACTAACCT
*
174587 AGTAGTTGTCTT
66 AGTAATTGTCTT
174599 TAAGGATGAAAAAGA
1 TAAGGATGAAAAAGA
174614 NNNNNNNNNN
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
76 14 0.16
77 72 0.84
ACGTcount: A:0.51, C:0.06, G:0.23, T:0.20
Consensus pattern (77 bp):
TAAGGATGAAAAAGAAAAAAAAAAAGATTAGTGAGAGGGAAGAAAAAATAAGCAGTAACTAACCT
AGTAATTGTCTT
Found at i:175788 original size:13 final size:13
Alignment explanation
Indices: 175754--175788 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
175744 ATATTGAAAA
175754 TATATTAATTTTT
1 TATATTAATTTTT
*
175767 TAT-TGAATTTTT
1 TATATTAATTTTT
175779 TATATTAATT
1 TATATTAATT
175789 AAAAAATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (13 bp):
TATATTAATTTTT
Found at i:182194 original size:17 final size:17
Alignment explanation
Indices: 182169--182205 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
182159 TATTCGGTTA
* *
182169 TTTTGTTATTTTACGAT
1 TTTTATTATTTTAAGAT
182186 TTTTATTATTTTAAGAT
1 TTTTATTATTTTAAGAT
182203 TTT
1 TTT
182206 ATCATTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.03, G:0.08, T:0.68
Consensus pattern (17 bp):
TTTTATTATTTTAAGAT
Done.